X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 20.0
Details PEG 4000, Acetate buffer, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.6 α = 90
b = 37.15 β = 115.43
c = 53.99 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV MIRROR/MONOCHROMATOR 1998-12-20
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44B2 -- SPRING-8 BL44B2

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.1 100 95.0 0.087 -- -- 5.2 41962 41962 -- 0.0 14.2
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.1 1.15 87.1 0.455 -- -- 3.0 890

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
-- 1.4 20.0 -- 0.0 21313 21313 1040 98.9 -- -- 0.224 0.275 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.4 1.49 -- 180 3298 0.325 0.344 0.026 97.5
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.8
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 3.18
x_scbond_it 2.14
x_mcangle_it 2.11
x_mcbond_it 1.3
x_improper_angle_d 1.14
x_dihedral_angle_d 26.9
x_angle_deg 1.5
x_bond_d 0.009
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Sigma A (Observed) 0.23
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.22
Luzzati Sigma A (R-Free Set) 0.22
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1019
Nucleic Acid Atoms 0
Heterogen Atoms 43
Solvent Atoms 73

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
SOLVE model building
SCALEPACK data reduction
DENZO data collection